.TH g_cluster 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_cluster - clusters structures

.B VERSION 4.5
.SH SYNOPSIS
\f3g_cluster\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-dm" " rmsd.xpm "
.BI "\-o" " rmsd\-clust.xpm "
.BI "\-g" " cluster.log "
.BI "\-dist" " rmsd\-dist.xvg "
.BI "\-ev" " rmsd\-eig.xvg "
.BI "\-sz" " clust\-size.xvg "
.BI "\-tr" " clust\-trans.xpm "
.BI "\-ntr" " clust\-trans.xvg "
.BI "\-clid" " clust\-id.xvg "
.BI "\-cl" " clusters.pdb "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]dista" ""
.BI "\-nlevels" " int "
.BI "\-cutoff" " real "
.BI "\-[no]fit" ""
.BI "\-max" " real "
.BI "\-skip" " int "
.BI "\-[no]av" ""
.BI "\-wcl" " int "
.BI "\-nst" " int "
.BI "\-rmsmin" " real "
.BI "\-method" " enum "
.BI "\-minstruct" " int "
.BI "\-[no]binary" ""
.BI "\-M" " int "
.BI "\-P" " int "
.BI "\-seed" " int "
.BI "\-niter" " int "
.BI "\-kT" " real "
.SH DESCRIPTION
\&g_cluster can cluster structures with several different methods.
\&Distances between structures can be determined from a trajectory
\&or read from an XPM matrix file with the \fB \-dm\fR option.
\&RMS deviation after fitting or RMS deviation of atom\-pair distances
\&can be used to define the distance between structures.


\&single linkage: add a structure to a cluster when its distance to any
\&element of the cluster is less than \fB cutoff\fR.


\&Jarvis Patrick: add a structure to a cluster when this structure
\&and a structure in the cluster have each other as neighbors and
\&they have a least \fB P\fR neighbors in common. The neighbors
\&of a structure are the M closest structures or all structures within
\&\fB cutoff\fR.


\&Monte Carlo: reorder the RMSD matrix using Monte Carlo.


\&diagonalization: diagonalize the RMSD matrix.


\&gromos: use algorithm as described in Daura \fI et al.\fR
\&(\fI Angew. Chem. Int. Ed.\fR \fB 1999\fR, \fI 38\fR, pp 236\-240).
\&Count number of neighbors using cut\-off, take structure with
\&largest number of neighbors with all its neighbors as cluster
\&and eleminate it from the pool of clusters. Repeat for remaining
\&structures in pool.


\&When the clustering algorithm assigns each structure to exactly one
\&cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
\&file is supplied, the structure with
\&the smallest average distance to the others or the average structure
\&or all structures for each cluster will be written to a trajectory
\&file. When writing all structures, separate numbered files are made
\&for each cluster.


\&Two output files are always written:

\&\fB \-o\fR writes the RMSD values in the upper left half of the matrix
\&and a graphical depiction of the clusters in the lower right half
\&When \fB \-minstruct\fR = 1 the graphical depiction is black
\&when two structures are in the same cluster.
\&When \fB \-minstruct\fR  1 different colors will be used for each
\&cluster.

\&\fB \-g\fR writes information on the options used and a detailed list
\&of all clusters and their members.


\&Additionally, a number of optional output files can be written:

\&\fB \-dist\fR writes the RMSD distribution.

\&\fB \-ev\fR writes the eigenvectors of the RMSD matrix
\&diagonalization.

\&\fB \-sz\fR writes the cluster sizes.

\&\fB \-tr\fR writes a matrix of the number transitions between
\&cluster pairs.

\&\fB \-ntr\fR writes the total number of transitions to or from
\&each cluster.

\&\fB \-clid\fR writes the cluster number as a function of time.

\&\fB \-cl\fR writes average (with option \fB \-av\fR) or central
\&structure of each cluster or writes numbered files with cluster members
\&for a selected set of clusters (with option \fB \-wcl\fR, depends on
\&\fB \-nst\fR and \fB \-rmsmin\fR).

.SH FILES
.BI "\-f" " traj.xtc" 
.B Input, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-dm" " rmsd.xpm" 
.B Input, Opt.
 X PixMap compatible matrix file 

.BI "\-o" " rmsd\-clust.xpm" 
.B Output
 X PixMap compatible matrix file 

.BI "\-g" " cluster.log" 
.B Output
 Log file 

.BI "\-dist" " rmsd\-dist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ev" " rmsd\-eig.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-sz" " clust\-size.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-tr" " clust\-trans.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-ntr" " clust\-trans.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-clid" " clust\-id.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cl" " clusters.pdb" 
.B Output, Opt.
 Trajectory: xtc trr trj gro g96 pdb cpt 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]dista"  "no    "
 Use RMSD of distances instead of RMS deviation

.BI "\-nlevels"  " int" " 40" 
 Discretize RMSD matrix in  levels

.BI "\-cutoff"  " real" " 0.1   " 
 RMSD cut\-off (nm) for two structures to be neighbor

.BI "\-[no]fit"  "yes   "
 Use least squares fitting before RMSD calculation

.BI "\-max"  " real" " \-1    " 
 Maximum level in RMSD matrix

.BI "\-skip"  " int" " 1" 
 Only analyze every nr\-th frame

.BI "\-[no]av"  "no    "
 Write average iso middle structure for each cluster

.BI "\-wcl"  " int" " 0" 
 Write all structures for first  clusters to numbered files

.BI "\-nst"  " int" " 1" 
 Only write all structures if more than  per cluster

.BI "\-rmsmin"  " real" " 0     " 
 minimum rms difference with rest of cluster for writing structures

.BI "\-method"  " enum" " linkage" 
 Method for cluster determination: \fB linkage\fR, \fB jarvis\-patrick\fR, \fB monte\-carlo\fR, \fB diagonalization\fR or \fB gromos\fR

.BI "\-minstruct"  " int" " 1" 
 Minimum number of structures in cluster for coloring in the xpm file

.BI "\-[no]binary"  "no    "
 Treat the RMSD matrix as consisting of 0 and 1, where the cut\-off is given by \-cutoff

.BI "\-M"  " int" " 10" 
 Number of nearest neighbors considered for Jarvis\-Patrick algorithm, 0 is use cutoff

.BI "\-P"  " int" " 3" 
 Number of identical nearest neighbors required to form a cluster

.BI "\-seed"  " int" " 1993" 
 Random number seed for Monte Carlo clustering algorithm

.BI "\-niter"  " int" " 10000" 
 Number of iterations for MC

.BI "\-kT"  " real" " 0.001 " 
 Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
